Manganese in PDB 1ovr: Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13

The structure of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13, PDB code: 1ovr was solved by L.Di Costanzo, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.888, 149.177, 38.578, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 30.5

The binding sites of Manganese atom in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 (pdb code 1ovr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13, PDB code: 1ovr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn50 b:23.4 occ:1.00 OE1 A:GLU36 1.8 32.1 1.0 ND1 A:HIS39 1.9 30.9 1.0 OE1 A:GLU10 2.2 29.1 1.0 OE2 A:GLU10 2.2 26.9 1.0 CD A:GLU10 2.5 19.9 1.0 CE1 A:HIS39 2.9 32.9 1.0 CG A:HIS39 3.0 32.3 1.0 CD A:GLU36 3.0 35.7 1.0 CB A:HIS39 3.3 29.3 1.0 OE2 A:GLU36 3.7 32.9 1.0 CA A:GLU36 3.9 25.7 1.0 CB A:GLU36 4.0 25.7 1.0 CG A:GLU10 4.0 21.7 1.0 NE2 A:HIS39 4.0 32.0 1.0 CD2 A:HIS39 4.1 32.5 1.0 CG A:GLU36 4.1 30.4 1.0 N A:GLU36 4.7 23.6 1.0 CD2 A:LEU13 4.7 24.2 1.0 CB A:GLU10 4.8 22.9 1.0 O A:GLU36 4.8 26.8 1.0 CA A:HIS39 4.9 28.9 1.0 C A:GLU36 4.9 26.9 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn51 b:27.0 occ:1.00 ND1 B:HIS39 2.0 16.8 1.0 OE1 B:GLU36 2.2 26.0 1.0 OE2 B:GLU10 2.3 28.7 1.0 OE1 B:GLU10 2.4 26.3 1.0 CE1 B:HIS39 2.6 18.2 1.0 CD B:GLU10 2.7 27.6 1.0 CG B:HIS39 3.2 21.3 1.0 CD B:GLU36 3.3 26.3 1.0 OE2 B:GLU36 3.6 30.6 1.0 CB B:HIS39 3.8 27.3 1.0 NE2 B:HIS39 3.8 16.9 1.0 CD2 B:HIS39 4.1 15.7 1.0 CG B:GLU10 4.2 29.3 1.0 CA B:GLU36 4.6 29.1 1.0 CG B:GLU36 4.6 25.1 1.0 CB B:GLU36 4.9 28.7 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn52 b:25.3 occ:1.00 OE2 D:GLU36 1.9 26.1 1.0 OE1 C:GLU10 2.1 22.8 1.0 OE1 C:GLU36 2.1 27.0 1.0 OE2 C:GLU10 2.1 25.8 1.0 ND1 C:HIS39 2.2 24.2 1.0 CD C:GLU10 2.4 20.5 1.0 CE1 C:HIS39 3.0 22.5 1.0 CD D:GLU36 3.1 33.7 1.0 CD C:GLU36 3.2 24.9 1.0 CG C:HIS39 3.2 28.2 1.0 CB C:HIS39 3.7 33.6 1.0 OE2 C:GLU36 3.7 21.5 1.0 OE1 D:GLU36 3.7 32.8 1.0 CG C:GLU10 3.9 26.9 1.0 NE2 C:HIS39 4.2 14.4 1.0 CG2 D:ILE32 4.2 29.2 1.0 CG D:GLU36 4.2 30.9 1.0 MN D:MN53 4.2 23.3 1.0 CD2 C:HIS39 4.3 23.9 1.0 OH D:TYR17 4.5 15.6 1.0 CG C:GLU36 4.5 26.7 1.0 CA C:GLU36 4.6 30.8 1.0 CD2 D:LEU13 4.7 27.5 1.0 CB C:GLU36 4.7 29.5 1.0 CB C:GLU10 4.8 31.1 1.0 CD2 C:LEU13 4.8 38.4 1.0 CG D:LEU13 4.9 28.1 1.0 CE1 D:TYR17 4.9 25.1 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn53 b:23.3 occ:1.00 OE1 D:GLU36 1.9 32.8 1.0 OE2 C:GLU36 1.9 21.5 1.0 ND1 D:HIS39 2.0 26.1 1.0 OE2 D:GLU10 2.0 26.0 1.0 OE1 D:GLU10 2.2 23.6 1.0 CD D:GLU10 2.4 24.0 1.0 CD D:GLU36 2.7 33.7 1.0 CE1 D:HIS39 2.8 25.4 1.0 CD C:GLU36 3.0 24.9 1.0 CG D:HIS39 3.1 27.2 1.0 OE2 D:GLU36 3.1 26.1 1.0 CB D:HIS39 3.5 26.0 1.0 OE1 C:GLU36 3.6 27.0 1.0 CA D:GLU36 3.9 28.0 1.0 CG D:GLU10 3.9 28.1 1.0 CG D:GLU36 3.9 30.9 1.0 NE2 D:HIS39 4.0 24.8 1.0 CB D:GLU36 4.0 28.1 1.0 CG2 C:ILE32 4.1 30.4 1.0 CD2 D:HIS39 4.1 23.3 1.0 CG C:GLU36 4.2 26.7 1.0 MN C:MN52 4.2 25.3 1.0 CD2 C:LEU13 4.2 38.4 1.0 OH C:TYR17 4.3 24.6 1.0 N D:GLU36 4.5 29.2 1.0 CE1 C:HIS39 4.7 22.5 1.0 CE1 C:TYR17 4.8 26.1 1.0 CB D:GLU10 4.8 30.0 1.0 O D:ASP35 4.9 29.4 1.0 CZ C:TYR17 4.9 25.0 1.0 C D:ASP35 5.0 28.8 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Four-Helix Bundle Model Di-Mn(II)-DF1-L13 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn54 b:90.7 occ:1.00 OE1 D:GLU44 2.1 62.5 1.0 OE2 D:GLU44 2.2 54.3 1.0 CD D:GLU44 2.4 57.0 1.0 CG D:GLU44 3.9 44.7 1.0 CB D:GLU44 4.7 33.8 1.0 O D:HOH61 4.8 21.4 1.0

S.Geremia, L.Di Costanzo, L.Randaccio, D.E.Engel, A.Lombardi, F.Nastri, W.F.Degrado. Response of A Designed Metalloprotein to Changes in Metal Ion Coordination, Exogenous Ligands, and Active Site Volume Determined By X-Ray Crystallography. J.Am.Chem.Soc. V. 127 17266 2005.
ISSN: ISSN 0002-7863
PubMed: 16332076
DOI: 10.1021/JA054199X